Variation in mRNA transcript levels in mice will be assessed using data from three microarray experiments that involve tissue samples from laboratory mice and are designed to quantify sources of variation within and across laboratory mouse strains and tissues. We will also develop variance estimation methods that improve upon existing methods. Microarray experiments can be designed to test a wide range of hypotheses, but the inferential power of subsequent analysis may not be fully realized without an understanding of variation in transcript abundance within and between individual mice of the same strain, between different strains, and between different tissues. Further study of variation in transcript abundance through experiments to study these sources of variation has great potential since important disease-related phenotypes have been shown to vary in inbred mice due to genetics, epigenetics, and biological factors.